An experiment that summarizes all our work!!!

Hi All:

As experts in Microbiology we must understand the whole meaning of our last experimental result (Figures 1 and 2).

Figure 1: Aspect of bacterial plates incubated in the Lab after 5 days at 30ºC.

Figure 2: Aspect of bacterial plates incubated in Paula’s drawer after 7 days at Room Temperature.

Analyzing the images we rapidly can undertand what we can interpret from the data and what we can conclude of our research. This is basic to perform our: Poster, Proceedings/Manuscript and Exposition.

Come on!!!  we are in the way to convince to the audience what we have inferred of our research. But, … First of all: we need to have Numbers for every bacteria (3G and 3I):

-Uv effect on bacterial growth (mean and margins!!!)

-Uv effect on mutation frequency (mean and margins).

Come on who is the first!!! I would like We’ll infer the numbers from the plates photographs. Use the blog!!!

I propose to discuss all this result in an extra session next week (14-18 March 2016).

See your email and wassap!!!

Francisco Martínez-Abarca

Departamento de Microbiología y Sistemas simbióticos.

Estación Experimental del Zaidín. CSIC.

Granada

 

We have a title for our work!!

Hi All:

The end of our research is really close. Last session we decided which is the title that explain the work performed. It was at the end of the morning. But it was a very important moment:

“Effect of ultra-violet light on the mutation frequency of a soil bacteria”.

All of us understood, what we already made. Try to determine if our “favourite” bacteria – Sinorhizobium meliloti- can serve as a test for evaluate the DNA damage caused by ultraviolet light exposure.

Now, we are close to the end, but… we need to put an extra effort to get it.

Fig 1.  Carmen and Cristina mixing bacterial culture previously to the uv treatments

In resources (see here), we have the current state of our “manuscript”.  We need to fill all the parts of our comunication (Highlights, Summary, Introduction, mat and methods, Results, Conclussions. It is extremely helpful to visit what students made last year (see here). 

Special focus should be made in the part of MY OWN IDEAS. This is a summary of the meaning of this project for everyone. 

You must think on it.

Come on, we are deal with the finishing of a Fantastic Project

Hip, hip Hurra!!!!

Francisco Martínez-Abarca
Departamento de Microbiología y Sistemas Simbióticos.
Estación Experimental del Zaidín. CSIC.
Granada

Reading into strange results

Last entry finished with:

“…We repeated the experiements over a new culture of 3G S. meliloti strain (I remind you the previous was 3I). In which every treatment (0, 15 and 30 seconds of uv) was made twice. Now, Plates are in Paula’s home (and also in the Lab).

Hopefully, these new results allow to determine uv effect more accurately. …”

The experiment performed was plates 1 and 4 no uv treatment; plates 2 and 5, 15’’ uv treatment; and plates 3 and 6, 30’’ uv treatment.

However,  last results did not show the expected numbers (Fig. 1). 

Fig 1: Aspect of all plates incubated at Paula’s home after 6 days at room temperature.  Numbers and dilutions performed are indicated in the last blog entry. 

Analyzing the plates we found that uv treatment was properly made on both groups of plates (those growing on Paula’s home and also the lab one). However, the plates to count the mutants present in every culture give an unexpected  high numbers,  even in the most diluted plates (see figure).

What is the explanation of this strange result? 

Have we got a different mut frequency in this experiment?

If we analyze the differences in the protocol with the previous experiment performed, we can inffer where it could be the problem. Also we can see in the previous blog (¿Dónde mutan los genes?) some clues about what could occur in this last experiments (particularly in the post Consecuencias del brain storming).

I would like we could discuss here in the blog what is happening; how we can avoid it and try to repeat properly the experiment (Next session 2nd of March).

I encourage you to give an answer. Who is the first?? (specially those who came on last experimental session).

Francisco Martínez-Abarca

Estación Experimental del Zaidín. CSIC.

Departamento de Microbiología y Sistemas Simbióticos.

Granada

When the mess is less mess

Last session confirm we are too much closer to the end of our Project. Again, we find out our Project deals with counting bacteria, don’t we?. But examining your faces yesterday  we also realized the meaning to count bacterial colonies in a plate: 

to know the number of bacteria present in a particular tube or treatment. 

All serial dilutions performed aim to obtain that number as accurate as posible. In this regard and analyzing the data obtained in the last experiment Paula’s home we could observe an interesting “tendency” in the data. Remind last experiment (see Figure 1).

Figure 1: This figure summarizes what we did in the previous sesión (18th Jan) and yesterday (16th Feb). A S. meliloti culture was distribuited to three plates and stress under uv treatments (0, 15’’ and 30’’). All further steps where designed in order to get the number of bacteria and mutants present in the different treatments.

As we could observed; some of the plates were a real mess (Lab plates see previos entry in the blog). However, after a detail analysis of Paula’s home bacteria plates we could obtain some numbers (see table 1):

Table 1: Colony counts of the respective dilutions and treatments performed

These numbers reflect an interesting result. If we interpret properly what they mean we can observe a clear effect on bacterial growth by uv treatment (Table 2)

 Table 2: Effect of uv treatment on bacterial counts

And also an astonishing “tendency” of the putative frequency of mutants on the plate’s uv treatments (Table 3)

Table 3: Effect of uv treatment on mutation frequency

All of us (teachers, coordinators, friends,  … included) must know how these data appear (all calculations performed). And, most important, we must be aware about the meaning and importance of this last result.

As expected in Science. Experiments must be reproducible. 

What we are waiting for next session?

We repeated the experiements over a new culture of 3G S. meliloti strain (I remind you the previous was 3I). In which every treatment 0, 15 and 30 seconds of uv) was made twice. Now, Plates are in Paula’s home (and also in the Lab).

Hopefully, these new results allow to determine uv effect more accurately.

Come on as I mention previosly the end of the Project is much closer.

And finally only mention that the PIIISA commission (in Granada) did not allowed to hold our next session of 2nd March in the PARQUE DE LAS CIENCIAS in Granada.

We’ll see in the EEZ next session.

Francisco Martínez-Abarca
Estación Experimental del Zaidín. CSIC.
Granada

When some experiments are a mess

Sometimes in Science the data you expect from your experiments do not appear. This is the reason why Biology, or Microbiology in this case, is an experimental Science. As you already know last experiments should have indicated a putative mutation frequency affected by the uv treatment. However, we have only data from the plates incubated at Paula’s Home (Fig. 1; 3I plates). The plates incubated in the Lab (3G plates) are a real mess!

 

Figure 1: images of the plates with identical dilutions of 3I (Paula’splates) and 3G (Labplates)isolates. Above plates indicating total bacteria (TY plates). Below plates indicating mutants in SacB gene (Sacarose plates). In 3G plates the bacterial spread was not properly done. Plates were not dried before to perform incubations.It is difficult to count colonies and to be sure of the dilutions performed.

Which is this difference of this result with the previous one (see last entries)?

 As I mention, something (just a Little detail) was wrong. I found out that the plate were humid when I saw one day later after incubation. This humidity is critical to form single colonies (also occur in previous experiments). Does it!!!.

However, in spite we can not yet estimate the mutant frequency. We can deduce that the experiments are, in principle,well performed. Uv treatments looks to have in effect on bacteria, and the dilutions calculated are probably right in order to get the accurate conclussions of our work.

Come onstudents!!

We have to planify the next experiments in order to avoid this error. Plates must be dry by standing opened for a while (3-5 min) before to close with parafilm and put in the incubators.

Again, next session is awaiting us!!

That is Science!! Be patients and consistents.

Francisco Martínez-Abarca

Estación Experimental del Zaidín. CSIC.

Granada